These options control formatting of alignments in results pages. The
default is HTML, but other formats (including plain text) are available.
PSSM and PssmWithParameters are representations of Position Specific Scoring Matrices and are only available for PSI-BLAST.
The Advanced view option allows the database descriptions to be sorted by various indices in a table.

Choose how to view alignments.
The default "pairwise" view shows how each subject sequence aligns
individually to the query sequence. The "query-anchored" view shows how
all subject sequences align to the query sequence. For each view type,
you can choose to show "identities" (matching residues) as letters or
dots.
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Format for PSI-BLAST: The Position-Specific Iterated BLAST (PSI-BLAST) program performs iterative searches with a protein query,
in which sequences found in one round of search are used to build a custom score model for the next round.
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Inclusion Threshold: This sets the statistical significance threshold for including a sequence in the model used
by PSI-BLAST to create the PSSM on the next iteration.